[adegenet-commits] r683 - pkg/R

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2010-10-07 17:53:12 +0200 (Thu, 07 Oct 2010)
New Revision: 683

Modified:
   pkg/R/dapc.R
Log:
Passing a very low tolerance to lda.default to avoid rescaling issues when conserving all the PCs.


Modified: pkg/R/dapc.R
===================================================================
--- pkg/R/dapc.R	2010-10-06 15:07:05 UTC (rev 682)
+++ pkg/R/dapc.R	2010-10-07 15:53:12 UTC (rev 683)
@@ -50,6 +50,7 @@
     ## get n.pca from the % of variance to conserve
     if(!is.null(perc.pca)){
         n.pca <- min(which(cumVar >= perc.pca))
+        if(perc.pca > 99.999) n.pca <- length(pcaX$eig)
         if(n.pca<1) n.pca <- 1
     }
 
@@ -68,7 +69,7 @@
 
 
      ## PERFORM DA ##
-    ldaX <- lda(XU, grp)
+    ldaX <- lda(XU, grp, tol=1e-30) # tol=1e-30 is a kludge, but a safe (?) one to avoid fancy rescaling by lda.default
     if(is.null(n.da)){
         barplot(ldaX$svd^2, xlab="Linear Discriminants", ylab="F-statistic", main="Discriminant analysis eigenvalues", col=heat.colors(length(levels(grp))) )
         cat("Choose the number discriminant functions to retain (>=1): ")
@@ -328,6 +329,19 @@
 
 
 
+
+
+############
+## crossval
+############
+crossval <- function (x, ...) UseMethod("crossval")
+
+crossval.dapc <- function(){
+
+}
+
+
+
 ###############
 ## randtest.dapc
 ###############